How to find internal stem-loop structure in a fasta file?

Question

[archana.bioinfo87]

Hi,

I have large data sets. In one file having more than 3000 fasta sequences. I want to check all the sequences. If any of the sequences forming internal stem-loop structure I want to exclude those sequences.

I am only familiar with R but unable to figure it out.

Any help is much appreciated.

Thanks

[Devon Ryan]

Are you expecting these to be RNA sequences, dsDNA sequences, or ssDNA?

[archana.bioinfo87]

I am expecting these in my 21 nucleotide RNA sequences

[Devon Ryan]

Have a look at RNAfold from the ViennaRNA package. It's command line rather than in R, but it's the most standard tool out there to look at RNA secondary structures.